Structural View of Biology

Enzymes

Enzymes are Nature's chemists, performing all of the chemical transformations needed for life. Enzymes catalyze chemical reactions by bringing together all of the necessary chemical tools in the proper place. They typically have an "active site" that captures the chemicals that will be modified, holding them in the perfect orientation to perform the chemical change. Researchers have separated the many types of enzymes into a few functional classes, based on the reactions that they perform. Click on any of the sub-categories below to explore a few examples of each enzyme class. You can also explore many other enzymes in the other functional categories in "Structural View of Biology."

Transferases are the cell's master builders, taking chemical groups and transferring them from one place to another. The reactions performed by transferases can be as simple as the addition of the sulfate group, or as complex as the processive addition of nucleotides to a growing DNA strand.

DNA polymerase plays the central role in the processes of life. It carries the weighty responsibility of duplicating our genetic information. Each time a cell divides, DNA polymerase duplicates all of its DNA, and the cell passes one copy to each daughter cell. In this way, genetic information is passed from generation to generation. Our inheritance of DNA creates a living link from each of our own cells back through trillions of generations to the first primordial cells on Earth. The information contained in our DNA, modified and improved over millennia, is our most precious possession, given to us by our parents at birth and passed to our children.

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Fat, these days, is a bad word. But we can't survive without fats, and more particularly, without fatty acids. Fatty acids are small molecules composed of a long string of carbon and hydrogen atoms, with an acidic group at one end. They are used for two essential things in your body. First, they are used to build the lipids that make up all of the membranes around and inside your cells. Second, fatty acids are a concentrated source of energy, so they are often connected to glycerol to form fats, which is a compact way to store energy until it is needed. But as we all know, if we eat too much, this extra fat can build up!

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We brush our teeth twice a day with fluoride toothpaste, use mouthwash, limit sugars in our diet...and we still get cavities. Cavities are caused by bacteria that consume some of the sugar in our diet, ferment it, and then release acids. These acids eat away at the hard minerals in our teeth. It seems like it would be easy to brush these bacteria away, and get rid of them once and for all. However, they have a trick to avoid this.

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Although it may not seem so during the holiday season, we do not have to eat continually throughout the day. Our cells do require a constant supply of sugars and other nourishment, but fortunately our bodies contain a mechanism for storing sugar during meals and then metering it out for the rest of the day. The sugars are stored in glycogen, a large molecule that contains up to 10,000 glucose molecules connected in a dense ball of branching chains. Your muscles store enough glycogen to power your daily activities, and your liver stores enough to feed your nervous system and other tissues all through the day and on through the night.

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Cells are great recyclers. They need to be, otherwise we would be faced with an insurmountable need for new molecular building blocks and enough energy to manage them. For instance, new messenger RNA chains are made constantly, transmitting information from the nucleus to build new proteins. Afterwards, these chains are broken down and the components are recycled. A complex set of salvage machinery is used to recycle these components.

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Methanogenic archaea produce about a billion tons of methane each year. Methanogens are tiny microbes similar to bacteria that colonize anaerobic environments such as the bottom of lakes and swamps or the gut of cows and humans. They feed on molecules like carbon dioxide, methanol and acetic acid that are produced by fermenting bacteria, and release methane as their waste product, bubbling up as marsh gas, or in the case of our own resident methanogens, less socially-acceptable gases.

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Cells use many methods to control their proteins, to make sure that they perform
their jobs when and where they are needed. Some are brutally irreversible, such as
the continuous breakdown of obsolete proteins by the
ubiquitin/proteasome
system. Others, such as the modulation of enzyme function by allosteric motions, are
far more subtle and respond to the second-by-second needs of the cell. Often,
chemical groups are added to amino acids in proteins to modulate their function.
Phosphate groups are a familiar example: they are widely used to turn signaling
proteins on and off, controlled by a diverse collection of kinases and phosphatases that
add and remove these regulatory phosphate groups.

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RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA. The enzyme RNA polymerase carries the weighty responsibility of creating all of these different RNA molecules.

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If you have visited your local health food store or looked closely at the ingredients in your daily multivitamin, you may have noticed that the element selenium is often listed as one of the beneficial supplements. Selenium is a double-edged sword, however. In general, selenium compounds are toxic and have an unpleasant garlicy odor, but in trace amounts, selenium is essential for our health. Selenium atoms are similar to sulfur atoms, with similar properties, except that selenium compounds tend to be more reactive. In a few specialized proteins, this extra reactivity is just what is needed. For instance, by using a selenium atom instead of sulfur, thioredoxin reductase improves its rate of catalysis by 100 times, and formate dehydrogenases act 300 times faster.

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Your body is a democratic nation of cells. Each cell is an individual with its own needs, but all of your cells work together to keep you alive. As you might imagine, this requires an incredible amount of cooperation. Cells are in constant communication to inform their neighbors of their needs and future plans. They send messages to each other, passing hormones and chemokines and other molecular messages from cell to cell. These messages are received by proteins in the cell membrane, which transmit the signal inside. There, a bewilderingly complex collection of proteins relays the message to all of the appropriate places inside the cell.

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Cells are master chemists. They perform all manner of chemical reactions to build and modify their molecules. One of the chemical tricks used by many cells is to add sulfuryl groups to a molecule. Under typical cellular conditions, sulfuryl groups carry a negative charge, and they have lots of oxygen atoms that accept hydrogen bonds from other molecules. This makes sulfurylated molecules much more soluble and easy to recognize. To build molecules with sulfuryl groups, cells use a diverse collection of sulfotransferases. These enzymes take a sulfuryl group from the convenient carrier molecule PAPS (3'-phosphoadenosine-5'-phosphosulfate), and transfer it to the target molecule.

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Phosphate groups are perfect chemical groups for
modifying the function of proteins: they have a strong negative charge, they are
fairly bulky, and they can form multiple hydrogen bonds. When a phosphate group
is attached or removed to a protein, it may modify the shape and flexibility of the
protein chain, or provide a readily-visible handle for recognition by other proteins.
Cells take full advantage of these possibilities, and in a typical cell, phosphate groups
are used to regulate the function of about one third of their proteins.

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